Halo: Brotherhood
by EBsayian
Summary: Set 15 yrs. after Halo 3. Chief has been away quelling the rebellion in the outer rim when he is allowed to come back to earth when a distress signal is emitted. After his party lands the officers aboard the ship here chief has went rogue. Is it true?
1. Betrayal

Halo: Brotherhood

This is set fifteen years after the events of Halo 3. Some things may be changed from halo cannon either because I don't know it or for the sake of the story. Here's hoping I can continue with a story. Please enjoy and Review.

Chapter 1: Betrayal

Journal Entry: Dr. Halsey May 2, 2517

The first generation of Spartans have been introduced. There are twelve of them and I have decided to name them each after the twelve disciples of Jesus of Nazareth. I have decided to name them this because just as the original twelve went out and developed a new religion, so while mine be remarked as the prototypes of a new type of soldier. Peter, Andrew, James, John, Philip, Matthew, Bartholomew, Thomas, Mark, Simon, Thaddaeus and Judas. Giving one of them the name Judas makes me feel uneasy. Although I am a believer in science, naming one of my precious Spartans a name of a betrayer still burdens me. My only hope is that they will not turn out as my notes predicated and die as they reach the age of pubescence or worse in that they might go rogue.

Journal Entry: Dr. Halsey April 17, 2558

My first generation of Spartans have all died when Reach fell. The only one I know for sure to be alive is John and there was no doubt in my mind that he would be. Other generations have been shipped off and are now safe until called in for battle. There is a sense of loss for those who died, like a mother losing her son. I know that I must strive forward and keep building the next generations of super soldiers in the hopes that they will be able to defeat the Covenant. But there will be none as perfect as my first.

Admiral Ollie R. Looper aboard his battle cruiser _The Iron Fist_ has been deployed out to the Outer Core in order to quiet tensions between the humans and the new beings living there, the Covenant. Frustration still resides within these souls after years of conflict and it will take nearly double of the time to wipe it away. Standing next to Admiral Ollie is the icon of the Halo Wars, Master Chief. He has been away in the outer core for nine years. The six before that, he was in cryogenic stasis along with Cortana after the destruction of the Ark. Cortana, after nine years he might see her again. At first, she was like a thorn in his side, but she began to… not be as irritating. He had heard through rumors she was now the top A.I. in the UNSC military and coordinated much of the militaries files with the help of lesser A.I.s.

An officer monitoring the communication channel hails Admiral Ollie. "Admiral, there seems to be a slight disturbance on Variath. It's just a few clicks from here."

The Admiral asks, "Are there any other ships in the area?"

"No sir."

"Chief, if you don't mind heading down there with a small scouting party."

"It would be my pleasure sir."

The planet Variath looked like a swap. The swamp water was so flooded that it came up above Chief's knees. Chief hated swamps as they reminded him of the first time he fought the flood… and met Guilty Spark. There was a small Covenant force here, but nothing the scouting party couldn't handle. That's what made this feel uncomfortable to the Spartan. For a distress call to be alerted, especially to hail a battle cruiser, there had to be a significant force. These were mostly Grunt and Jackals. Even a standard company could handle these enemies. Then on his radar Chief noticed something. It was significantly larger and didn't move like any Brute or Covenant. "Guard the perimeter," the Spartan tells his teammates. "I'll scout ahead." He raises his assault rifle and trudges through the thick swamp.

A few yards ahead Chief notices that the blip on his radar is coming toward him, due East. He turns waiting for the attack. The blip comes closer. Ten meters… seven meters… five meters… yet he saw nothing. He switched to his night vision to get a clearer look, but there was nothing but trees and water. The blip was now right on top of him. Then it hit Chief, the water. Water gushes forth as something bursts out. Chief fires a few rounds at the thing.

The officers hear the firing of Chief's assault rifle and wonder if they should pursue. They stay frozen in time waiting for the Spartan to emerge from the mist. Emerge he does. "What happened, Chief," asks one of the soldiers.

"Brute tried to sneak up on me," replies the Spartan, "and failed."

"Good to hear." The officer puts his index finger and middle finger to his ear where his comm. piece is. "This is scouting party Alpha to base, all clear. We are heading to evac for transport." The officer releases the button on the earpiece. "All right men let's move out."

The men begin to move forward when Chief calls to the officer. "Sergeant!" The officer turns around to be sniped in the head. The other officers look on in disbelief.

"What the hell… we're on the same side!"

"Who said I'm on yours." The Chief begins to fire upon his crew and they unleash there bullets back, but lack of experience and of armor prove that the officers are no match for the Spartan. One of them has a bullet in his leg. Master Chief walks over to him. The Spartan hears one of the communications officers yelling at him in his comm. device. "Chief, what's wrong!"

"Tell the military I'm no longer there puppet." The Spartan takes off his comm. device and holds it near to the screaming officer after stepping on his bullet wound. "Let this show that Master Chief has declared war with the UNSC." The officer jumps as he hears the gunshot that silences the scream. Admiral Ollie looks at his communications officer.

"Well? What is it private?"

The private looks at his superior dumbfounded. "I think Master Chief just betrayed us."


	2. Escape

Halo: Brotherhood

Chapter Two: Escape

Master Chief roams around the swamp looking for the Pelican that took him to this planet. The creature that leaped out at him had knocked him out. Later, he awoke to find a Brute floating upside down in the water. Well, at least he got it. He had gone back to see that the troops that were with him in the scouting party, dead. He thought that there must have been more of the Brutes and they killed his teammates. He took their dog tags so that their families could receive and remember them. It was the least he could do. He finally found the Pelican with the ramp open. He swept the entire ship before taking off to make sure nothing Covenant was aboard. The Chief then started the engine and headed back to the _Iron Fist_.

Within minutes he was inside the ships docking bay with a company of soldiers waiting outside for him. He opened the hatch expecting a greeting, but instead received rifle barrels pointed at his face. Not willing to raise his hands or anything the Chief looks toward Admiral Ollie. "Care to fill me in, sir."

With a stern look Ollie replies back, "Did you expect a welcoming party after killing those men Chief."

The Spartan stood stunned. "What?"

"You heard me soldier. Why did you kill those men?"

"Whatever has happened your mistaken. I awoke from a black out to see those men dead in the swamp."

"Really? Care to explain this then." The captain holds a recording of the voice communications with the Chief declaring all out war on the UNSC before killing his comrade. Sierra 117 stands stunned with nothing to say. "If it were up to me I would kill you where you stand. Be thankful I'm not as unmoral as you."

"Sir, I didn't kill those men."

"The UNSC will be the judge of that." Admiral Ollie motions for his men to slap electrosynthesized handcuffs on the Chief. Reluctantly they do. The hero they had all looked up to for more than eighteen years had betrayed them and was now being handcuffed.

Later the _Iron Fist_ lands on Earth and the Master Chief is taken in to UNSC headquarters for questioning. He approaches the Secretary of War of the UNSC, Joseph Connery. "Never that I'd see you here Chief," says the General.

"You and me both."

"Good to see you again Chief. Wish it could be under better circumstances."

Chief looked over to see a full figured form of a holographic Cortana standing next to the Secretary of War. For years she had been his ally on the field of battle and now she would be the one to condemn him to death.

"Cortana," asks Joseph.

"Yes, sir."

"Bring up the report."

A holographic screen appears in front of the general and he begins to scroll through it. "It says here that during a mission to discover the origin of a distress beacon you killed all your squad mates and immediately afterward declared war on the UNSC."

"Sir, you know better than anyone that I would give my life for this war. What makes you think that I would kill the people that I fought for so long to protect?"

"I don't know, but there is one sure way to find out. Cortana jack into the Chief's security visor and see if we have video of what happened." The video shows Chief wading through the water when it goes black. "Cortana?"

"Seems to be some kind of EMP interference. Wait. Here's where it starts again."

Chief then stares in disbelief as the camera attached to his helmet shows him gunning down his own men. "What do you have to say for yourself?"

"That I'm innocent."

"You're joking," says the Secretary. "Even after video surveillance shows you committing the act you're still holding onto your illusion of innocence."

"It's not an illusion sir. It's the truth."

"Take him to a holding cell." Guards come up and take Master Chief away. The Secretary of War turns. "I know what you're thinking Cortana, but this isn't the Chief we used to know. He's changed."

"I know sir; it's just hard to believe."

"It is for me too."

Chief is held in a force field generated cell thinking about what he just saw. He had no recollection of this atrocity, yet there he was on the monitor, shooting and killing his comrades. Maybe he had done this unconsciously. "Maybe I deserve this."

"The hell you do." The Chief looks around.

"Cortana?"

"Were you expecting the Arbitar?"

"How are you communicating with me?"

"I'm wirelessly interfacing with your communication device inside your helmet. I have a wireless network of about five miles. If there's anything electronic, I can interface with it. Chief, if there's one thing I know is that you would kill yourself, before you would ever harm one of your brothers in arms. That's why I'm getting you out of here."

"Not sure if that's a good idea."

"Too late I've already opened your cell. Now move it soldier!"

"When General Joseph finds out they'll destroy your circuit."

"Not if I come with you. The training room is your next right."

"Why go there?"

"Because they have tranq guns." Chief opens the room to find a bunch of weapons. As he exits the room he has tranq clips loaded into his pistol and battle rifle. In his pocket he has bullet clips for use if there's any danger later. "Here we are together again. Just like old times."

"If you mean by old times that the UNSC and the remnant of the Covenant are after us then, yeah, I guess so." Chief sees some UNSC soldiers up ahead and uses his tranq gun to take them out. He then maneuvers down the hall and is about to turn the corner when he hears something. A group of five men fully armed are making their rounds and are walking towards the Chief. They turn the corner and see nothing as they continue walking. After their gone, the Spartan releases his death grip on the pipes near the ceiling falling back to the floor. He continues to walk down a hall when he gets to a room full of armed soldiers. "Cortana, a little help." Suddenly Cortana's voice comes over the intercom inside the room. All men intently listen.

"Attention all personal Captains Pike, Picard, and Tirk require their crew to be on deck immediately." The men begin to scramble as they hurry out the other side. "Am I good or what."

"Just stay focused on getting me to the nearest exit."

"It only gets harder from here Spartan. But I have a way of sliding things to your favor. Suddenly the lights go out. Chief then sees a door open and lights turning on showing a path. "Just follow the trail."

The Secretary of War looks around confused as he sees the lights are out. "Cortana give me an update."

"It seems that Sierra 117 has escaped. I can't locate him. He's injected some sort of virus into my system and I'm going to have to start shutting down certain facilities in order to quarantine it."

"Like which ones," asks the general.

"Security, lights, and communication. You know nothing of value."

"This is no time for sarcasm. Destroy that virus and start getting things back up and running."

"I'm going as fast as I can sir."

Master Chief is able to move past soldiers silently without peaking their interest as he makes his way to an exit. He then hears Cortana over his comm. channel. "I deserve an acting award."

"What?"

"Oh nothing, make a right up here." The Chief comes to the garbage disposal room.

"Really," asks Chief.

"Did you expect to waltz out the front door." Without second guessing Cortana again Chief opens a chute and dives down into the muk.

"Cortana, status report."

"Sorry sir, I'm with the Chief on this one."

"What!"

"We're going to find proof of his innocence and bring it back here."

"Cortana I'm going to wipe your entire system until you are completely gone."

"Yeah, I'm not going to stick around for that. Sorry for the inconvenience sir." Cortana's hologram disappears from the central hub of the computer. The Secretary slams his fist down on the table. "Get everyone on red alert. I want them found. You three," the general points three men on a computer. "See if you can trace her signal."

"Uh, sir." The men move out of the way so the general can see their computers. On their screens is Cortana doing an akanbe with her tongue sticking out. The veins in the general's head is about to pop.

Chief gets a jolt of electricity and cold as Cortana fully transfers over to his system. "Home sweet, home. So, what do we do now?"

The Chief replies to here as he exits from the sewer into the rising sun, "We go see an old friend."

Alright people I know it's been sort of slow, but stick with me because I promise it will get more interesting. Next chapter we start to get more involved with what is going on unless I don't get enough reviews that is. Come on, read and review even if you don't like it. Criticize me if you want. I believe that's the only way to become a better writer. (I accept praise too). If you like this story or any of my others you may want to look my newly formed comic book company on facebook. Just go to this .?#!id=100001321216861&ref=search

Or search for Zine Comics and we've got the blue logo with the yellow letters that says our name. Thanks and I hope you enjoy it.


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